When there is a power outage, the pumps will ofcourse stop pumping water from the sump, but the water in the main tanks will continue to drain from the main tanks to the sump untill it can not go over the overflows plus......also, if the return spouts are below the water level, they will start to syphon water from the 2 tanks back to the sump untill the water level goes below the spouts. Best to have a small hole in the return tubes right at the operateing level inside the main tanks so that air can get in and break/stop the syphoning.
So.....In the sump when operateing, the water level must stay low enough so that when power fails, it will be able to hole the drainage and syphonage ( is syphonage a word, haha ) from the main tanks without overflowing the sump and causeing a mess on the floor.
I agree that 2 pumps may be best....the two tanks will not HAVE to have the same flow, only if you want it or the livestock needs it.....most likely with a 40g sump, neither tank will have enough flow because it may run dry if you use too big of pumps....not sure how much flow 'you' are going to want in your tanks.....
Both tanks will be as one system so yes, if there is toxins or parisites ect, in one and is water born, then it will all mix together in the sump and go to both tanks.....
Refugiums are IMO a good thing.......